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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctttgatccttgaaactaacccaagtcagctcagctctgttttctttccaggggccatatactgtagcgacctgtttcctttttctgctagtatatgactatacgttacctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCATCACAAACACCATCCCTCTGAAGGAGGAGAAGAGTTTTCCGCAGCTGACT

Basic information

species Zea mays
transcript GRMZM2G038791_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038791_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g03540.1 (Oryza sativa), 3'ss of exon 7
gtatgctttgatccttgaaactaacccaagtcagctcagctctgttttctttccaggggccatatactg-tagcgacctgtttcctttttctgctag---tata-tgactatacgttacctttc-cagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCATCACAAACACCATCCCTCTGAAGGAGGAGAAGAGTTTTCCGCAGCTGACT
                             | |    ||||   | |  | |||| |     | ||     |   |   ||||   ||| | ||  |    |||| |   | ||| || |||||  |||||| |||||||| |||||| |||||||||| ||||| ||||||||||||||||||||||| || ||||| |||||||| |||||||| ||||||||||||
----------------------------tgactatgcagcaaagataacgttcctgacattaaatttgactcatgctttgttatttttctgtggaaaatttataatatttgtacattgcctttttcagCCCGCCCGCCATTGAAAGGTTATCAAGTGGTTTGTTTCAAGAAGTAATCATCACAAACACTATACCTCTCAAGGAGGACAAGAGTTTCCCGCAGCTGACT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211009691|gb|FL435043.1|FL435043
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|211126323|gb|FL371824.1|FL371824
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGKTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|60338563|gb|DN205536.1|DN205536
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|91052223|gb|EB162641.1|EB162641
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|19770111|gb|BQ034832.1|BQ034832
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|74243299|gb|DT651213.1|DT651213
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|78085035|gb|DV513428.1|DV513428
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCCCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|60350838|gb|DN217811.1|DN217811
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|71429935|gb|DR810985.1|DR810985
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|76011084|gb|DT938254.1|DT938254
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|93016209|gb|EB641729.1|EB641729
EST:     CAGGAAGGCGCCCGAGAAGTATAGGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|211276932|gb|FL386926.1|FL386926
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|86468618|gb|DY234988.1|DY234988
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|78544258|gb|DV621756.1|DV621756
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|211123271|gb|FL408205.1|FL408205
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|110204864|gb|EC886761.1|EC886761
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|60398185|gb|DN231001.1|DN231001
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|78125653|gb|DV544037.1|DV544037
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|78544420|gb|DV621918.1|DV621918
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|211292499|gb|FL395084.1|FL395084
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|76914465|gb|DV165541.1|DV165541
EST:     CAGGAAGGCGCCCGAGAAATATATGCTTGCTGCACACAGGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|19769635|gb|BQ034356.1|BQ034356
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
EST: gi|26457160|gb|CA828743.1|CA828743
EST:     CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAG                         CCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT
genomic: CAGGAAGGCGCCCGAGAAGTATATGCTTGCTGCACACATGGTGTTTTTAGgtatgctttg ... acctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagcgacctgtttcctttttctgctagtatatgactatacgttacctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCATCACAAACACCATCCCTCTGAAGGAGGAGAAGAGTTTTCCGCAGCTGACT
                                           ttacctttcc  CT-rich tract
                          tagtatat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctttgatccttgaaactaacccaagtcagctcagctctgttttctttccaggggccatatactgtagcgacctgtttcctttttctgctagtatatgactatacgttacctttccagCCCACCCGCCATCGAAAGGCTATCAAGTGGATTGTTCCAAGAAGTAATCATCACAAACACCATCCCTCTGAAGGAGGAGAAGAGTTTTCCGCAGCTGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA